Transcript Dmitriev Cybertaxonomy and revisionary systematics

Cybertaxonomy and
revisionary systematics
Dmitry Dmitriev
Illinois Natural History Survey, USA
http://taxonworks.org/
Taxonomy
• During last 255 years since Linnaeus about
1,800,000 species have been described
• Descriptive taxonomy remains very slow and
labor intensive process
Species accumulation curve
•Catalogue of Life provides records for ~1,350,000 species names
•Total estimated at 1,800,000 species
Number of species described in 10 years periods
•Estimated 10,000-15,000 species described each year
Species accumulation curve in
Cicadellidae
Species accumulation curve in
Cicadellidae: Typhlocybinae
Number of species of Typhlocybinae
described in 10 year periods
•Dworakowska
•Anufriev
•Ross
•Beamer
•Edwards
•Osborn
•Ribaut
•Matsumura
•Knull
•Zachvatkin
•Ross
•Young
•Dworakowska
•Dietrich
•Dmitriev
Taxonomic impediment
• Despite our best efforts, the vast majority
(perhaps 90% or more) of the species remain
undocumented.
• Taxonomists currently describe 15,000 new
species per year.
• Recent estimates suggest that between
27,000 and 130,000 species are being lost
each year to extinction.
Taxonomic revision challenges
• A taxonomic revision summarizes knowledge about a
group of organisms (morphology, distribution
patterns, ecological preferences, bioacoustics,
molecular variation, synonyms, new species, tools
for identifications, etc.)
• Efficient management and synthesis of large
amounts of nomenclatural, morphological, and
distributional data is required.
Number of species of Typhlocybinae
described in 10 year periods
•Dworakowska
•Anufriev
•Ross
•Beamer
•Edwards
•Osborn
•Ribaut
•Matsumura
•Knull
•Zachvatkin
•Ross
•Young
•Dworakowska
•Dietrich
•Dmitriev
Taxonomic revision challenges
• When published, a revision provides a snap-shot of the modern
knowledge on a group of organisms.
• It stimulates further study and species discovery.
• It quickly becomes outdated.
• 2006: First record of the tribe Erythroneurini from
South America. Description of the genus Zyginama
• 2008: Revision of the genus
Zyginama (70 species)
•2013: Three new species of the
genus Zyginama from Argentina
What is cybertaxonomy?
• Technological advances, including relational
databases, digital imaging, and Internet
dissemination, provide taxonomists with tools to
increase both the quality and quantity of such
studies.
• Cybertaxonomy aims to develop information
processing tools that enable taxonomists both to
produce traditional taxonomic revisions more rapidly
and to develop new models for managing and
disseminating taxonomic information.
Available applications
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3i
SpeciesFile
MX
Scratchpads
3i - Interactive keys
3i – Pictorial keys
3i - Dichotomous Keys
3i - Taxonomic pages
Publications based on 3i
3i - Data Sharing
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Catalogue of Life (CoL)
Encyclopedia of Life (EoL)
Global Biodiversity Information Facility (GBIF)
Discover Life
Global Name Architecture (GNA)
• Biodiversity Heritage Library
SpeciesFile
•Designed by David Eades
and colleagues in the
Illinois Natural History
Survey (USA)
•Supported by
International Orthoptera
Society
•Online application based
on SQL Server database
and Visual Basic.net.
•Originally designed for the
insect order Orthoptera, but
later was adopted by
researchers working on
other insect groups.
Species File
•System allows storage
and retrieval of taxonomic
and nomenclatural
information with
associated images,
distribution, and
bibliography information.
•System strictly enforces
the rules of the
International Code of
Zoological Nomenclature.
•Data shared with
Catalogue of Life, GBIF
MX (MatriX)
•Designed by Matt
Yoder in Texas A&M
University (USA)
•Based on MySQL
and Ruby on Rails
online application.
•Originally designed
for the insect order
Hymenoptera, but
later was adopted by
researchers working
on other insect
groups.
MX (MatriX)
•The system could be
used for storage and
manipulation of
different types of
data: bibliographies,
images, specimen
records, distribution,
molecular and
morphological
information.
•Dichotomous and
matrix based keys.
•Images could be
linked to MorphBank.
MX (MatriX)
•Significant part of MX is an
integrated morphological
ontology builder which
allows to link vocabulary
terms to each other, as well
as their definitions and
illustrations.
MX (MatriX)
•Dichotomous and
matrix based keys.
Scratchpads
• Based on Drupal content
management system
• Online application which
provides users with templates
to enter taxonomy related
information in uniform way
• Support for classifications,
taxon profiles, specimens,
literature, images, maps,
phenotypic, genotypic &
morphometric datasets, keys,
phylogenies
• Data could be exported in
various formats
Publishing observations and taxon
data
Pushed to GBIF & EOL
Specimen records & species
pages on Scratchpads
(requires site registration with
GBIF & EOL)
Darwin
Core
Archive
(DwCA)
Article publishing
XML submission, peer review &
marked-up publication by Pensoft
HTML
XML
doi:10.3897/zookeys.50.539
PDF
Paper assembled from
Scratchpad database
Published in Zookeys & Phytokeys
TaxonWork: new development
TaxonWork: new development
Sources
Georeferences
People
Collecting Events
Media
Specimens
Taxon Concepts
Matrices
Taxon Name
Alternative Classification
Interactive Keys
Name Statuses
Relationships
TaxonWorks: Nomen Ontology
https://github.com/SpeciesFileGroup/nomen
TaxonWorks: Nomen Ontology
https://github.com/SpeciesFileGroup/nomen
TaxonWork: new development
Acknowledgements
•Collaborators: Christopher Dietrich, Roman Rakitov,
Daniela Takia, Sindhu Krishnankutti, Doris Lagos, David
Eades, Matt Yoder, Edward DeWalt, Alexey Solodovnikov,
Yalin Zhang, Richard Pile, and many others.
•Grant support: NSF, EoL.